In InstallShield 2019 R2, you can now use the Package Support Framework that applies runtime fixes such as the File Redirection Fixup and Custom Fixup in MSIX.
File Redirection Fixup - You can use the File Redirection Fixup to redirect attempts to write or read data in a directory that isn't accessible from an application that runs in an MSIX container.
Custom Fixup - You can use the Custom Redirection Fixup that will solve application compatibility issues with a configuration file that specifies the fixes that you want to apply to your application.